Early inbreeding depression, i.e. embryonic recessive lethals, eliminates a large proportion of selfed progeny during embryo development. A model of early inbreeding depression suggested that in most conifers the variation between genotypes in the number of lethals rather than the variation in the actual rate of self-fertilization accounts for the variation between selfing rates at the seed stage. Polyembryony, the formation of several embryos per ovule in conifers, diminished the fitness cost of embryonic lethals and allowed embryo competition. We studied variation in the outcrossing rate at the seed stage in an experimental population of Scots pine. Despite extensive variation, pollen production of the trees, which is expected to predict the probability of self-fertilization, did not account for the low selfing rate variation at the seed stage. The genotypes having lowest numbers of embryonic lethals had the highest selfing rates at the seed stage. Early inbreeding depression maintains a very low selfing rate at the seed stage and masks the correlation between the rate of selffertilization and the selfing rate at the seed stage. This is typical of most conifers and can also be common among perennial angiosperm species.